Interferon-alpha/beta binding fusion proteins and therapeutic uses thereof

ABSTRACT

Polypeptides and multimeric polypeptides capable of binding interferon α and/or interferon β which are useful therapeutically in methods of treating interferon α/β-related conditions or diseases.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit under 35 USC §119(e) of U.S. Provisional 60/691,551 filed 17 Jun. 2005, which application is herein specifically incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The invention encompasses interferon α- and/or β-binding fusion proteins, as well as therapeutic uses of such polypeptides for inhibiting interferon α and/or β activity, especially the interferon α proteins.

2. Description of Related Art

It has previously been reported that a humanized anti-interferon α antibody neutralizes human leukocyte interferon and is beneficial in rodent models of insulin-dependent diabetes mellitus (IDDM) (Chuntharapai et al. (2001) Cytokine 15(5):250-260).

BRIEF SUMMARY OF THE INVENTION

In a first aspect, the invention features a nucleic acid molecule encoding an interferon α- and/or interferon β-binding fusion protein (R1)_(x)-(R2)_(y)-F, wherein R1 comprises the extracellular domain of interferon alpha receptor 1 (IFNAR1) component, R2 comprises the extracellular domain of interferon receptor alpha 2 (IFNAR2) component, F is a fusion component, and x and y are each independently a positive integer ≧1, for example between 1 and 10. The extracellular domains of the wild-type human IFNAR1 (SEQ ID NO:2 including signal peptide 1-27) and IFNAR2 (SEQ ID NO:4 including signal peptide 1-26) proteins are encoded by the nucleic acid sequences shown in SEQ ID NO:1 and 3, respectively.

The components of the fusion protein may be arranged in different orders, for example, F-R1-R2 R1-F-R2, R2-F-R1, R2-R1-F, etc. More specifically, R1 is derived from an IFNAR1 component that comprises amino acids 28-436 or 28-335 of SEQ ID NO:2, or a fragment thereof, optionally modified with one or more modifications defined in modification group I, and R2 is an IFNAR2 component comprising 27-243 or 35-233 of SEQ ID NO:4, or a fragment thereof, optionally modified with one or more of the modifications of modification group II. Optionally, (R1)_(x)-(R2)_(y)-F further comprises a signal sequence (SS).

R1: Naturally occurring wild-type IFNAR1 protein is a 557-amino acid protein having the amino acid sequence of the extracellular domain shown in SEQ ID NO:2 with signal sequence included at 1-27. In one embodiment, R1 comprises amino acids 28-436 of SEQ ID NO:2 optionally further modified by one or more modifications listed in modification group 1. In another embodiment, R1 comprises amino acids 28-335 of SEQ ID NO:2, or a fragment thereof, optionally comprising at least one of modification from modification group I.

Modification Group I: an amino acid at position S90, S91, L92, K93, V96, Y97, W156, L305, R306, and/or V307 of SEQ ID NO:2 is replaced with a different amino acid.

R2: Naturally occurring human wild-type IFNAR2 protein is a 515-amino acid protein having the amino acid sequence of the extracellular domain shown in SEQ ID NO:4 with signal sequence included at 1-26. In one embodiment, R2 comprises amino acids 27-243 of SEQ ID NO:4 optionally with at least one of the modification selected from those listed in modification group II. In another embodiment, R2 comprises 35-233 of SEQ ID NO:4, or a fragment thereof, optionally modified with one or more of the modifications listed in modification group II.

Modification Group II: amino acid at position M73, P76, L79, V107, V109, W127, I130, E111, S123, H124, N125, D131, D165, D216, E77, K75, E104, H103, Y70, W99, Y106, I72, L95, F126, and/or L128 of SEQ ID NO:4 is (are) replaced with a different amino acid.

The optional fusion component (F) comprises any component that enhances the functionality of the fusion protein. Thus, for example, a fusion component may enhance the biological activity of the fusion protein, aid in its production and/or recovery, or enhance a pharmacological property or the pharmacokinetic profile of the fusion protein by, for example, enhancing its serum half-life, tissue penetrability, lack of immunogenicity, or stability. In preferred embodiments, the fusion component is selected from the group consisting of a multimerizing component, a serum protein, or a molecule capable of binding a serum protein.

When the fusion component is a multimerizing component, the fusion component includes any natural or synthetic sequence capable of interacting with any other multimerizing component to form a higher order structure, e.g., a dimer, a trimer, etc. In specific embodiments, the multimerizing component is selected from the group consisting of (i) an immunoglobulin-derived domain, (ii) an amino acid sequence between 1 to about 500 amino acids in length, optionally comprising at least one cysteine residue, (iii) a leucine zipper, (iv) a helix loop motif, and (v) a coil-coil motif. In a specific embodiment, the immunoglobulin-derived domain is selected from the group consisting of the Fc domain of IgG or the heavy chain of IgG. In another specific embodiment, the Fc domain of IgG is human FcΔ1(a), an Fc molecule comprising a mutation of the region involved in forming the disulfide bond with the light chain.

When the fusion component is a serum protein, the serum protein may be any serum protein or a fragment of a serum protein. When the fusion component is a molecule capable of binding a serum protein, it may be a small molecule, a nucleic acid, a peptide, or an oligosaccharide. The fusion component may also be a protein such as Fc gamma R1, ScFv, etc. In preferred embodiments, the fusion component is encoded by the nucleic acid that encodes the fusion protein of the invention. In some embodiments, however, such as when the fusion component is an oligosaccharide, the fusion component is attached post-translationally to the expressed fusion protein.

The nucleic acid molecule of the invention may further optionally comprise a signal sequence (SS) component. When a SS is part of the polypeptide, any SS known to the art may be used, including synthetic or natural sequences from any source, for example, from a secreted or membrane bound protein. In a preferred embodiment, an ROR signal sequence is used (SEQ ID NO:5).

In specific embodiments, the invention features a nucleic acid molecule encoding an interferon α- and/or interferon β-binding fusion protein, including nucleic acid molecules encoding an amino acid sequence selected from the group consisting of SEQ ID NO:6 (R2₂₇₋₂₄₃-R1₂₈₋₄₃₆-Fc) and SEQ ID NO:9 (R2₃₅₋₂₃₃-R1₂₈₋₃₃₅-Fc). In one embodiment, the nucleic acid molecule of the invention encodes a fusion protein capable of binding interferon α2a (IFNα2a).

In a related second aspect, the invention features a vector comprising a nucleic acid molecule of the invention. In third and fourth aspects, the invention encompasses expression vectors comprising the nucleic acid molecules operatively linked to an expression control sequence, and host-vector systems for the production of a fusion protein that comprise the expression vector, in a suitable host cell; host-vector systems, wherein the suitable host cell is, without limitation, a bacterial, yeast, insect, mammalian or plant cell, such as tobacco; or animals such as cows, mice, or rabbits. Examples of suitable cells include E. coli, B. subtilis, BHK, COS and CHO cells. Fusion proteins modified by acetylation or pegylation are also encompassed by the invention.

In a fifth aspect, the invention features a method of producing a fusion protein of the invention, comprising culturing a host cell transfected with a vector wherein the vector comprises a nucleic acid molecule of the invention, under conditions suitable for expression of the protein from the host cell, and recovering the protein so produced.

In a sixth aspect, the invention features an interferon α- and/or β-binding fusion protein comprising (R1)_(x)-(R2)_(y)-F, wherein R1, R2, F, x and y are as described above. X and y are preferably each a number between 1-3; preferably x and y are each 1. In specific embodiments, the fusion protein is an amino acid sequence selected from the group consisting of SEQ ID NO:6 and 9.

In a seventh aspect, the invention features a multimeric polypeptide, comprising two or more fusion proteins of the invention. In a specific embodiment, the multimeric polypeptide is a dimer. The dimeric interferon α- and/or β-binding fusion proteins of the invention are capable of binding interferon α and/or β (“α/β”) with an affinity of at least 10⁻⁸ M, as determined by assay methods known in the art. Generally, the ability of the dimeric interferon α/β-binding fusion proteins to inhibit (e.g., block) the biological activity of interferon α/β, may be measured, for example, by bioassay, such as an ELISA assay, for free and/or bound ligand. Bioassays may include luciferase-based assays using an ISRE promoter element, and/or interferon α/β stimulation of cell lines such as plasmocytoid dendritic cells (PDCs). Alternatively, a bioassay may involve the inhibition of the growth-inhibitory effect of interferon on cell lines such as Daudi.

In an eighth aspect, the invention features pharmaceutical compositions comprising a fusion protein of the invention with a pharmaceutically acceptable carrier. Such pharmaceutical compositions may comprise a monomeric or multimeric polypeptide, or nucleic acids encoding the fusion protein.

The interferon α/β-binding polypeptides of the invention are therapeutically useful for treating any disease or condition which is improved, ameliorated, or inhibited by removal, inhibition, or reduction of interferon α and or interferon β. These polypeptides are particularly useful for the treatment of autoimmune diseases, such as systemic lupus erythematosus (SLE) or insulin-dependent diabetes mellitus (IDDM), which are improved, ameliorated, or inhibited by removal, inhibition, or reduction of interferon α/β. Accordingly, in a further aspect, the invention features a therapeutic method for the treatment of an interferon α/β-related disease or condition, comprising administering a fusion protein of the invention to a subject suffering from an interferon α/β-related disease or condition. Although any mammal can be treated by the therapeutic methods of the invention, the subject is preferably a human patient suffering from or at risk of suffering from a condition or disease which can be improved, ameliorated, inhibited or treated with a fusion protein of the invention.

Other objects and advantages will become apparent from a review of the ensuing detailed description.

DETAILED DESCRIPTION OF THE INVENTION

Before the present methods are described, it is to be understood that this invention is not limited to particular methods, and experimental conditions described, as such methods and conditions may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.

As used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise. Thus for example, a reference to “a method” includes one or more methods, and/or steps of the type described herein and/or which will become apparent to those persons skilled in the art upon reading this disclosure and so forth.

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to describe the methods and/or materials in connection with which the publications are cited.

DEFINITIONS

The term “affinity for” interferon α/β means that the multimeric fusion proteins of the invention binds the intended cytokine(s) with an affinity of at least 10⁻⁸ M, preferably at least 10⁻⁹ M, even more preferably at least 10⁻¹⁰ M as determined by assay methods known in the art, for example, surface plasmon resonance, e.g., Biacore™ analysis. In some cases, binding to a specific cytokine (for example, α2) will be preferred.

The term “human interferon α” includes 23 or more closely related proteins encoded by distinct genes with a high degree of structural homology (Weismann et al (1986) Prog. Nucl. Acid. Res. Mol, Biol. 33:251 and (1993) J. Inteferon Res. 13;443-444; Roberts et al (1998) J. Interferon Cytokine Res. 18:805-816). The multimers of the invention preferably bind and inhibit interferon α2a, and may bind and inhibit other members of the interferon α family of proteins. The term “capable of specifically blocking interferon α” or “capable of inhibiting the activity of interferon α” and/or “capable of specifically blocking interferon β” or “capable of inhibiting the activity of interferon β”, means the interferon α/β-binding fusion proteins of the invention form multimers that inhibit the biological activity of the target cytokines, as measured, for example, by bioassay such as, for example, an ELISA assay, for free and/or bound ligand. Bioassays may include luciferase-based assays using an ISRE promoter element, and/or interferon α and or interferon β stimulation of cell lines such as PDCs. “IC50” is defined as the concentration of fusion protein required to inhibit 50% of the response to interferon α as measured in a bioassay. The multimeric fusion protein of the invention is capable of specifically binding to interferon α2a, with an affinity of at least about 10⁻⁹ M, or preferably at least about 3×10⁻¹⁰ M, and/or is capable of specifically binding to interferon β with an affinity of at least about 10⁻¹⁰ M, or preferably at least about 5×10⁻¹¹ M as determined by Biacore™ analysis. Alternatively, the ability of the multimeric polypeptide of the invention to inhibit interferon α and β activities may be expressed as IC50 which is the concentration of interferon α/β-specific multimeric protein that inhibits 50% of interferon α/β activity, as measured, for example, in a bioassay such as the ISRE-luciferase assay described below. The interferon α/β-specific multimeric polypeptides of the invention exhibit an IC50 in an interferon α2a assay of 1×10⁻⁸ M, more preferably 1×10⁻⁹ M, and in an interferon β bioassay of 1×10⁻⁹ M, more preferably 1×10⁻¹⁰ M.

The terms “treatment”, “treating”, and the like are used herein to generally include obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or partially preventing a disease, condition, or symptoms thereof, and/or may be therapeutic in terms of a partial or complete cure for a disease or condition and/or adverse effect attributable to the disease or condition. “Treatment” as used herein covers any treatment of a disease or condition of a mammal, particularly a human, and includes: (a) preventing the disease or condition from occurring in a subject which may be predisposed to the disease or condition but has not yet been diagnosed as having it; (b) inhibiting the disease or condition, i.e., arresting its development; or (c) relieving the disease or condition, i.e., causing regression of the disease or condition. The population of subjects treated by the method of the invention includes subjects suffering from the undesirable condition or disease, as well as subjects at risk for development of the condition or disease.

By the term “therapeutically effective dose” is meant a dose that produces the desired effect for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, for example, Lloyd (1999) The Art, Science and Technology of Pharmaceutical Compounding).

As used herein, a “condition or disease” generally encompasses a condition of a mammalian host, particularly a human host, which is undesirable and/or injurious to the host. Thus, treating a condition or disorder with an interferon α- and/or interferon β-binding fusion protein will encompass the treatment of a mammal, in particular, a human, who has symptoms reflective of elevated or deleterious interferon α/β, or who is expected to have such decreased activation in response to a disease, condition or treatment regimen. Treating an interferon α/β-related condition or disease encompasses the treatment of a human subject wherein reducing interferon α/β levels with the fusion protein of the invention results in amelioration of an undesirable symptom resulting from the interferon α/β-related condition or disease.

General Description

Studies in animals lacking interferon α/β have indicated that these cytokines play both overlapping and additive roles in the resistance to viral infections, inhibit cell proliferation and regulate expression of MHC class I. Elevated interferon α correlates with the development of human autoimmune disease (for review, see Stewart et al. (2003) Cytokine & Growth Factor Reviews 14:139-154). There is a very good correlation between the presence of interferon α and SLE and IDDM. Interferon a has also been associated with psoriasis (Schmid et al. (1994) J. Interferon Res. 14:229-234) and Crohn's disease (Fais et al. (1994) J. Interferon Res. 14:235-238). The present invention provides novel polypeptides, both monomers and multimers, capable of acting as interferon α/β-binding fusion proteins or antagonists capable of binding interferon α/β and blocking these biological actions.

Nucleic Acid Constructs and Expression

The present invention provides for the construction of nucleic acid molecules encoding interferon α/β-binding polypeptides. As described above, the nucleic acid molecules of the invention encode modified fragments of the wild-type (or naturally occurring) human IFNAR1 and/or IFNAR2 proteins. Accordingly, the nucleic acid molecules may be termed “recombinant”, “artificial”, or “synthetic” as they are not nucleic acid molecules found in nature, e.g., not naturally occurring sequences, but are sequences constructed by recombinant DNA technology.

These nucleic acid molecules are inserted into a vector that is able to express the fusion proteins of the invention when introduced into an appropriate host cell. Appropriate host cells include, but are not limited to, bacterial, yeast, insect, and mammalian cells. Any of the methods known to one skilled in the art for the insertion of DNA fragments into a vector may be used to construct expression vectors encoding the fusion proteins of the invention under control of transcriptional and/or translational control signals.

Expression of the nucleic acid molecules of the invention may be regulated by a second nucleic acid sequence so that the molecule is expressed in a host transformed with the recombinant DNA molecule. For example, expression may be controlled by any promoter/enhancer element known in the art. Promoters which may be used to control expression of the chimeric polypeptide molecules include, but are not limited to, a long terminal repeat (Squinto et al. (1991) Cell 65:1-20); SV40 early promoter region, CMV, M-MuLV, thymidine kinase promoter, the regulatory sequences of the metallothionine gene; prokaryotic expression vectors such as the beta-lactamase promoter, or the tac promoter (see also Scientific American (1980) 242:74-94); promoter elements from yeast or other fungi such as Gal 4 promoter, ADH, PGK, alkaline phosphatase, and tissue-specific transcriptional control regions derived from genes such as elastase I.

Expression vectors capable of being replicated in a bacterial or eukaryotic host comprising the nucleic acid molecules of the invention are used to transfect the host and thereby direct expression of such nucleic acids to produce the fusion proteins of the invention. Transfected cells may transiently or, preferably, constitutively and permanently express the polypeptides of the invention. When the polypeptide so expressed comprises a fusion component such as a multimerizing component capable of associating with a multimerizing component of a second polypeptide, the monomers thus expressed multimerize due to the interactions between the multimerizing components to form a multimeric polypeptide (WO 00/18932, herein specifically incorporated by reference).

The fusion proteins of the invention may be purified by any technique known in the art. When the polypeptides of the invention comprise a multimerizing component, which spontaneously forms a multimer with another polypeptide, the purification techniques used allow for the subsequent formation of a stable, biologically active multimeric polypeptide, also known as a “fusion protein”. For example, and not by way of limitation, the factors may be recovered from cells either as soluble proteins or as inclusion bodies, from which they may be extracted quantitatively by 8M guanidinium hydrochloride and dialysis (see, for example, U.S. Pat. No. 5,663,304). In order to further purify the factors, conventional ion exchange chromatography, hydrophobic interaction chromatography, reverse phase chromatography or gel filtration may be used.

R1 and R2 Components

Interferon α and interferon β bind to a common receptor sometimes known as the IFNα/βR made up of two subunits (IFNAR1 and IFNAR2). Naturally occurring wild-type IFNAR1 protein is a 557-amino acid protein having the extracellular amino acid sequence of SEQ ID NO:2 (shown with signal sequence). R1 is an IFNAR1-derived component having amino acids 28-436 or amino acids 28-335 of SEQ ID NO:2, or a fragment thereof. Naturally occurring human wild-type IFNAR2 protein is a 515-amino acid protein having the amino acid sequence of the extracellular domain shown in SEQ ID NO:4. R2 is an IFNAR2-derived component having amino acids 27-243 or amino acids 35-233 of SEQ ID NO:4, or a fragment thereof. Optionally, either or both components can be further modified to provide fusion proteins with specifically desired properties, such as, for example, improved solubility, reduced immunogenicity, improved PK, improved production characteristics, and/or improved ability to block interferon α and/or interferon β activity.

Fusion Components

The fusion proteins of the invention comprise a fusion component (F) that, in specific embodiments, is selected from the group consisting of a multimerizing component, a serum protein, or a molecule capable of binding a serum protein. When F comprises a multimerizing component, it includes any natural or synthetic sequence capable of interacting with another multimerizing component to form a higher order structure, e.g., a dimer, a trimer, etc. The multimerizing component may be selected from the group consisting of (i) a multimerizing component, (ii) a truncated multimerizing component, (iii) an amino acid sequence between 1 to about 500 amino acids in length, (iv) a leucine zipper, (v) a helix loop motif, and (vi) a coil-coil motif. When F is a multimerizing component comprising an amino acid sequence between 1 to about 500 amino acids in length, the sequence may contain one or more cysteine residues capable of forming a disulfide bond with a corresponding cysteine residue on another fusion protein comprising an F with one or more cysteine residues.

In a preferred embodiment, the multimerizing component comprises one or more immunoglobulin-derived domains from human IgG, lgM or IgA. In specific embodiments, the immunoglobulin-derived domain is selected from the group consisting of the Fc domain of IgG or the heavy chain of IgG. The Fc domain of IgG may be selected from the isotypes IgG1, IgG2, IgG3, and IgG4, as well as any allotype within each isotype group. In a specific embodiment, F is the Fc domain of IgG4 with Ser 228 (Cabot numbering) mutated to Pro to stabilize covalent dimer formation (Mol. Immunol. (1993) 30:105-108) and/or Leu235→Glu which eliminates residual effector functions (Reddy et al. (2000) J. Immunol. 164:1925-1933). In a preferred embodiment, F is the Fc domain of IgG1, or a derivative thereof which may be modified for specifically desired properties (see, for example, Armour et al. (2003) Mol. Immunol. 40:585-593; Shields et al. (2001) J. Biol. Chem. 276:6591-6604). In specific embodiments, the interferon α/β-binding polypeptide of the invention comprises one or two Fc domain(s) of IgG1.

In one embodiment, F is a serum protein or fragment thereof and is selected from the group consisting of α-1-microglobulin, AGP-1, orosomuciod, α-1-acid glycoprotein, vitamin D binding protein (DBP), hemopexin, human serum albumin (hSA), transferrin, ferritin, afamin, haptoglobin, α-fetoprotein thyroglobulin, α-2-HS-glycoprotein, β-2-glycoprotein, hyaluronan-binding protein, syntaxin, C1R, C1q a chain, galectin3-Mac2 binding protein, fibrinogen, polymeric Ig receptor (PIGR), α-2-macroglobulin, urea transport protein, haptoglobin, IGFBPs, macrophage scavenger receptors, fibronectin, giantin, Fc, α-1-antichyromotrypsin, α-1-antitrypsin, antithrombin III, apolipoprotein A-I, apolipoprotein B, β-2-microglobulin, ceruloplasmin, complement component C3 or C4, CI esterase inhibitor, C-reactive protein, cystatin C, and protein C. In a specific embodiment, F is selected from the group consisting of α-1-microglobulin, AGP-1, orosomuciod, α-1-acid glycoprotein, vitamin D binding protein (DBP), hemopexin, human serum albumin (hSA), afamin, and haptoglobin. The inclusion of an F component may extend the serum half-life of the interferon α/β-binding polypeptide of the invention when desired. See, for example, U.S. Pat. Nos. 6,423,512, 5,876,969, 6,593,295, and 6,548,653, herein specifically incorporated by reference in their entirety, for examples of serum albumin fusion proteins. hSA is widely distributed throughout the body, particularly in the intestinal and blood components, and has an important role in the maintenance of osmolarity and plasma volume. It is slowly cleared in the liver, and typically has an in vivo half-life of 14-20 days in humans (Waldmann et al. (1977) Albumin, Structure Function and Uses; Pergamon Press; pp. 255-275).

When F is a molecule capable of binding a serum protein, the molecule may be a synthetic small molecule, a lipid or liposome, a nucleic acid, including a synthetic nucleic acid such as an aptomer, a peptide, or an oligosaccharide. The molecule may further be a protein, such as, for example, FcγR1, FcγR2, FcγR3, polymeric Ig receptor (PIGR), ScFv, and other antibody fragments specific for a serum protein.

Optional Spacers

Components of the fusion proteins of the invention may be connected directly to each other or be connected via spacers. Generally, the term “spacer” (or linker) means one or more molecules, e.g., nucleic acids or amino acids, or non-peptide moieties, such as polyethylene glycol, which may be inserted between one or more component domains. For example, spacer sequences may be used to provide a desirable site of interest between components for ease of manipulation. A spacer may also be provided to enhance expression of the fusion protein from a host cell, to decrease steric hindrance such that the component may assume its optimal tertiary structure and/or interact appropriately with its target molecule. For spacers and methods of identifying desirable spacers, see, for example, George et al. (2003) Protein Engineering 15:871-879, herein specifically incorporated by reference. A spacer sequence may include one or more amino acids naturally connected to a receptor component, or may be an added sequence used to enhance expression of the fusion protein, provide specifically desired sites of interest, allow component domains to form optimal tertiary structures and/or to enhance the interaction of a component with its target molecule. In one embodiment, the spacer comprises one or more peptide sequences between one or more components that are between 1-100 amino acids, preferably 1-25. In a specific embodiment, the spacer is a two amino acid sequence. The two amino acid sequence can be Ser Gly or Arg Ser.

Inhibition of Interferon α/β Biological Activity

The fusion proteins of the invention are capable of inhibiting the biological activity interferon α with an IC50 (concentration of fusion protein required to inhibit 50% of the response to interferon α/β) of at least 1×10⁻⁸ M, more preferably 1×10⁻⁹ M for interferon α2a, and in an interferon β bioassay of 1×10⁻⁹ M, more preferably 1×10⁻¹⁰ M in an ISRE luciferase assay. Other bioassays useful to determine IC50 are known to the art, including for example, Daudi viability, and/or interferon α/β stimulation of PDCs.

Therapeutic Uses

The fusion proteins of the invention are therapeutically useful for treating any disease or condition which is improved, ameliorated, inhibited or prevented by removal, inhibition, or reduction of one or both of interferon α and β. Interferon α and interferon β both independently, and jointly, have been implicated in a variety of clinical conditions, such as SLE and IDDM. Accordingly, the blocking of these responses by the fusion protein will be useful for the treatment of any disease or condition in which there is increased level of interferon α/β.

In one embodiment, the interferon α/β-binding fusion protein is used to treat SLE. Data derived from animal experiments and examination of humans suffering from SLE implicate interferon α. Patients with SLE have ongoing interferon α production and serum interferon α levels are correlated with both diseases activity and severity (Ronnblom and Alm (2003) Arthritis Res. Ther. 5:68-75).

Suitable Subject for Treatment

A suitable subject for treatment is a human diagnosed as suffering from specific conditions improved by inhibition or reduction of interferon α/β, including autoimmune diseases such as SLE or IDDM.

Combination Therapies

In numerous embodiments, the fusion proteins of the invention may be administered in combination with one or more additional compounds or therapies. For example, multiple fusion proteins can be co-administered, or one polypeptide can be administered in conjunction with one or more therapeutic compounds. When a polypeptide of the invention binds interferon α/β, the one or more other therapeutic agent is one that is used to prevent or treat a condition associated with the presence of interferon α/β. A benefit of the combined use of the fusion protein of the invention with a second therapeutic agent is that combined use can provide improved efficacy and/or reduced toxicity of either therapeutic agent.

Methods of Administration

The invention provides methods of treatment comprising administering to a subject an effective amount of a fusion protein of the invention. In a preferred aspect, the fusion protein is substantially purified (e.g., substantially free from substances that limit its effect or produce undesired side-effects). The subject is preferably a mammal, and most preferably a human.

Various delivery systems are known and can be used to administer an agent of the invention, e.g., encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the compound, receptor-mediated endocytosis (see, e.g., Wu and Wu, 1987, J. Biol. Chem. 262:4429-4432), construction of a nucleic acid as part of a retroviral or other vector, etc. Methods of introduction can be enteral or parenteral and include but are not limited to intradermal, intramuscular, intra-articular, infusion proteineritoneal, intravenous, subcutaneous, intranasal, intraocular, and oral routes. The compounds may be administered by any convenient route, for example by infusion or bolus injection, by absorption through epithelial or mucocutaneous linings (e.g., oral mucosa, rectal and intestinal mucosa, etc.) and may be administered together with other biologically active agents. Administration can be systemic or local. Administration can be acute or chronic (e.g. daily, weekly, monthly, etc.) or in combination with other agents. Pulmonary administration can also be employed, e.g., by use of an inhaler or nebulizer, and formulation with an aerosolizing agent.

In another embodiment, the active agent can be delivered in a vesicle, in particular a liposome, in a controlled release system, or in a pump. In another embodiment where the active agent of the invention is a nucleic acid encoding a protein, the nucleic acid can be administered in vivo to promote expression of its encoded protein, by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e.g., by use of a retroviral vector (see, for example, U.S. Pat. No. 4,980,286), by direct injection, or by use of microparticle bombardment, or coating with lipids or cell-surface receptors or transfecting agents, or by administering it in linkage to a homeobox-like peptide which is known to enter the nucleus (see e.g., Joliot et al., 1991, Proc. Natl. Acad. Sci. USA 88:1864-1868), etc. Alternatively, a nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination. Systemic expression may also be achieved by plasmid injection (intradermally or intramuscularly) and electroporation into cells.

In a specific embodiment, the pharmaceutical compositions of the invention are administered locally to an area in need of treatment; this may be achieved, for example, and not by way of limitation, by local infusion during surgery, topical application, e.g., by injection, by means of a catheter, or by means of an implant, the implant being of a porous, non-porous, or gelatinous material, including membranes, such as sialastic membranes, fibers, or commercial skin substitutes.

A composition useful in practicing the methods of the invention may be a liquid comprising an agent of the invention in solution, in suspension, or both. The term “solution/suspension” refers to a liquid composition where a first portion of the active agent is present in solution and a second portion of the active agent is present in particulate form, in suspension in a liquid matrix. A liquid composition also includes a gel. The liquid composition may be aqueous or in the form of an ointment.

In one embodiment, the pharmaceutical composition of the invention is a sustained release composition. Sustained release formulations for delivery of biologically active peptides are known to the art. For example, U.S. Pat. No. 6,740,634, herein specifically incorporated by reference in its entirety, describes a sustained-release formulation containing a hydroxynaphtoic acid salt of a biologically active substance and a biodegradable polymer. U.S. Pat. No. 6,699,500, herein specifically incorporated by reference in its entirety, discloses a sustained-release formulation capable of releasing a physiologically active substance over a period of at least 5 months.

Diagnostic and Screening Methods

The fusion proteins of the invention may be used diagnostically and/or in screening methods. For example, the fusion protein may be used to monitor levels of interferon α/β during a clinical study to evaluate treatment efficacy. In another embodiment, the methods and compositions of the present invention are used to screen individuals for entry into a clinical study to identify individuals having, for example, too high or too low a level of interferon α/β. The fusion proteins of the invention can be used in methods known in the art relating to the localization and activity of interferon α/β, e.g., imaging, measuring levels thereof in appropriate physiological samples, in diagnostic methods, etc.

The fusion proteins of the invention may be used in in vivo and in vitro screening assays to quantify the amount of non-bound interferon α/β present, e.g., for example, in a screening method to identify test agents able to decrease the expression of interferon α/β. More generally, the fusion proteins of the invention may be used in any assay or process in which quantification and/or isolation of interferon α/β is desired.

Pharmaceutical Compositions

The present invention also provides pharmaceutical compositions comprising a fusion protein of the invention. Such compositions comprise a therapeutically effective amount of one or more fusion protein(s), and a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable” means approved by a regulatory agency of the Federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly, in humans. The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the therapeutic is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations and the like. Examples of suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin.

The fusion protein of the invention can be formulated as neutral or salt forms. Pharmaceutically acceptable salts include those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.

The amount of the fusion protein that will be effective for its intended therapeutic use can be determined by standard clinical techniques based on the present description. In addition, in vitro assays may optionally be employed to help identify optimal dosage ranges. Generally, suitable dosage ranges for intravenous administration are generally about 0.02-10 milligrams active compound per kilogram body weight. Suitable dosage ranges for intranasal administration are generally about 0.01 pg/kg body weight to 10 mg/kg body weight. Effective doses may be extrapolated from dose-response curves derived from in vitro or animal model test systems. The amount of compound administered will, of course, be dependent on the subject being treated, on the subject's weight, the severity of the affliction, the manner of administration, and the judgment of the prescribing physician. The therapy may be repeated intermittently while symptoms are detectable or even when they are not detectable.

Cellular Transfection and Gene Therapy

The present invention encompasses the use of nucleic acids encoding the fusion proteins of the invention for transfection of cells in vitro and in vivo. These nucleic acids can be inserted into any of a number of well-known vectors for transfection of target cells and organisms. The nucleic acids are transfected into cells ex vivo and in vivo, through the interaction of the vector and the target cell facilitated by lipid mixes or electroporation. The compositions are administered (e.g., by injection into a muscle) to a subject in an amount sufficient to elicit a therapeutic response. An amount adequate to accomplish this is defined as “a therapeutically effective dose or amount.”

In another aspect, the invention provides a method of reducing interferon α/β levels in a human or other animal comprising transfecting a cell with a nucleic acid encoding a polypeptide of the invention, wherein the nucleic acid comprises an inducible promoter operably linked to the nucleic acid encoding the polypeptide. For gene therapy procedures in the treatment or prevention of human disease, see for example, Van Brunt (1998) Biotechnology 6:1149-1154.

EXAMPLES

The following example is put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the methods and compositions of the invention, and are not intended to limit the scope of what the inventors regard as their invention. Efforts have been made to ensure accuracy with respect to numbers used (e.g., amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is average molecular weight, temperature is in degrees Centigrade, and pressure is at or near atmospheric.

Example 1 Construction of Interferon α/β-Binding Fusion Proteins

To create the parental interferon α/β-binding fusion protein, R2-R1-Fc (SEQ ID NO:6 and SEQ ID NO:9) nucleic acid encoding the human IFNAR1 extracellular domain (SEQ ID NO:2) and the human IFNAR2 extracellular domain (SEQ ID NO:4), each component having a N-terminal two amino acid restriction linker, were amplified using standard PCR techniques, and were ligated into an expression vector which contained the human Fc sequence, thus creating a fusion protein having the IFNAR1 and/or IFNAR2, and the hinge, CH2 and CH3 regions of human IgG1 from the N to C terminus. All sequences were verified by standard molecular biology techniques. The appropriate coding sequence was subcloned into a eukaryotic expression vector using standard molecular biology techniques.

Interferon α/β-binding fusion protein variants are created by site-directed mutagenesis of the parent fusion protein using techniques known to the art, and confirmed by sequencing.

Example 2 Determination of Interferon α/β Binding Affinity

The affinity of the interferon α/β-binding fusion proteins for human interferon α2A and human interferon β is measured using surface plasmon resonance (Biacore 2000™ or Biacore 3000™, as described in WO00/75319, herein specifically incorporated by reference in its entirety. Briefly, the interferon α/β-binding fusion proteins of the invention are captured onto the chip surface using anti-human Fc antibodies. Various concentrations of human interferon α and/or β are injected over the surface and the time course of association and dissociation are monitored. Kinetic analyses using BIA evaluation software are performed to obtain the association and dissociation rate constants.

The Biacore assays for the parental R2-R1-Fc (SEQ ID NO:6) construct relative to R1-Fc (SEQ ID NO:7) and R2-Fc (SEQ ID NO:8) were conducted. R1-Fc was found to have minimal binding activity. Table 1 shows the results obtained with R2-Fc, R2-R1-Fc, and R2(35-233)-R1(28-335)-Fc. TABLE 1 Construct Ligand K_(D) R2-Fc (SEQ ID NO: 8) IFNα-2a   1.0 × 10⁻⁸ M IFNβ   8.3 × 10⁻⁹ M R2-R1-Fc (SEQ ID NO: 6) IFNα-2a  1.2 × 10⁻¹⁰ M IFNβ 3.99 × 10⁻¹¹ M R2(35-233)-R1(28-335)-Fc (SEQ ID NO: 9) IFNα-2a 2.85 × 10⁻¹⁰ M IFNβ 8.29 × 10⁻¹² M

Example 3 Inhibition of Interferon α/β Bioactivity by Interferon α/β-Binding Fusion Proteins

HEK 293 cells transiently transfected with an ISRE-luciferase expression vector were used to determined the inhibitory effect of the fusion proteins of the invention on interferon α and interferon β activity. Briefly, HEK293 cells were transiently transfected using lipofectamine with a vector containing an ISRE-luciferase expression cassette. After 3 days at 37° C. various concentrations of interferon α/β-binding fusion proteins were added along with 50 pM of IFN-2A or IFN-β. The cells were then incubated at 37° C., with 5% CO₂ for 6 hours and the luciferase activity was determined using Steady-Glo, following the manufacturers instructions (Promega). IC50 values were determined as the concentration of interferon α/β-binding fusion protein that blocked 50% of the activity of interferon α or interferon β, and the values are shown in Table 2. TABLE 2 Construct Ligand IC50 R2-Fc (SEQ ID NO: 8) IFNα-2a 4.93 × 10⁻⁸ M IFNβ 5.48 × 10⁻⁸ M R2-R1-Fc (SEQ ID NO: 6) IFNα-2a 2.93 × 10⁻⁹ M IFNβ 8.31 × 10⁻¹¹ M  R2(35-233)-R1(28-335)-Fc IFNα-2a 4.91 × 10⁻⁹ M (SEQ ID NO: 9) IFNβ 1.12 × 10⁻¹⁰ M 

Alternatively, the inhibition of interferon α/β bioactivity by interferon α and interferon β-binding fusion proteins of the invention can be measured in Daudi cells. Briefly, Daudi cells are grown the presence of variable concentrations of interferon α/β-binding fusion proteins and 9 pM of human interferon 2a. Three days following IFN-2a addition, cell number is quantitated using CCK-8, following the manufacturers instructions (Dojindo). No inhibition was observed with R2-Fc, whereas R2-R1 -Fc exhibited an IC50 of about 1.3-3.3×10⁻⁸ M. 

1. A nucleic acid molecule encoding fusion protein (R1)_(x)-(R2)_(y)-F, wherein R1 is a human interferon a receptor 1 (SEQ ID NO:2) or a fragment or variant thereof, R2 is human interferon α receptor 2 (SEQ ID NO:4) or a fragment or variant thereof, F is a fusion component, and x and y are each independently a positive integer ≧1.
 2. The nucleic acid molecule of claim 1, wherein x and y are each
 1. 3. The nucleic acid of claim 1, wherein F is selected from the group consisting of a multimerizing component, a serum protein, or a molecule capable of binding a serum protein.
 4. The nucleic acid of claim 3, wherein F is a multimerizing component comprising an immunoglobulin-derived domain
 5. The nucleic acid of claim 4, wherein the immunoglobulin-derived domain is selected from the group consisting of the Fc domain of IgG or the heavy chain of IgG.
 6. A fusion protein (R1)_(x)-(R2)_(y)-F encoded by the nucleic acid molecule of claim
 1. 7. A fusion protein (R1)_(x)-(R2)_(y)-F, wherein R1 is a human interferon α receptor 1 (SEQ ID NO:2) or a fragment or variant thereof, R2 is human interferon α receptor 2 (SEQ ID NO:4) or a fragment or variant thereof, F is a fusion component, and x and y are each independently a positive integer ≧1.
 8. The fusion protein of claim 7 having an amino acid sequence selected from the group consisting of SEQ ID NO:6 or SEQ ID NO:9.
 9. A multimeric protein comprising two or more of the fusion proteins of claim
 7. 10. A vector comprising the nucleic acid molecule of claim
 1. 11. A host-vector system comprising the vector of claim 10, in a suitable host cell.
 12. A method of producing a fusion protein, comprising culturing the host-vector system of claim 11 under conditions suitable for expression of the protein from the host cell, and recovering the polypeptide so produced. 